Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A3 F76 I0 R1
|
30 |
23.0 |
980404 |
89.1% |
873539 |
142.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
NC_000913 |
1,785,179 |
A→T |
100% |
I645N (ATC→AAC) |
ppsA ← |
phosphoenolpyruvate synthetase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | NC_000913 | 1,785,179 | 0 | A | T | 75.4%
| 33.3
/ 5.4
| 20 | I645N (ATC→AAC) | ppsA | phosphoenolpyruvate synthetase |
| Reads supporting (aligned to +/- strand): ref base A (1/4); new base T (4/11); total (5/15) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
GCTCGGCCAGCAAGGCGTTGGACGGGATTTCACACATCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACA‑GTCGCGGAAGCTGTCGGAAACATAGCGGCCCGCGCCACGGAAGCCGAGCATCGGGTTCTCTTCAT > NC_000913/1785045‑1785317
|
gCTCGGCCAGCAAGGCGTTGGACGGGATTTCACACATCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGAtc < 1:454273/143‑1 (MQ=255)
ggCCAGCAAGGCGTTGGACGGGATTTCACACATCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATCTCaa < 1:4495/143‑1 (MQ=255)
ggctagtcGTTGGACGGGACTTCACTCCTCCTGCTGATTTTCAGCCCTTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGtt < 2:389868/136‑1 (MQ=255)
cgcccggCGTTGGCCGGGATTTCCCACCTCATGCTGCTTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGtt < 2:351756/138‑1 (MQ=255)
agccGTTGGACGGGATTCCACACATCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGCTCGTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTc < 2:347007/140‑1 (MQ=255)
ggACCGGACTTCACACATCATGCTGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCa < 1:271484/143‑1 (MQ=255)
gcgcgtgcacacaTCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATCTCAACGTTGGTCAGTCCCATGTc < 1:241993/136‑1 (MQ=255)
catGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGtt > 1:399079/1‑143 (MQ=255)
gttgatTTGCCGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCa < 2:23418/141‑1 (MQ=255)
ctcactttCCGCCCGTTCCCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCAc < 2:336515/138‑1 (MQ=255)
gactttCCGCCCGTTCTCGCCACGTCTCCGCCCCTGCCGCGCCAGCTCTCCAACCACCGCTGTCGCCTGACCTCCGGTACGCACGAGCGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTg < 2:263800/140‑1 (MQ=255)
cACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGaaa < 1:461879/143‑1 (MQ=255)
gTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACA‑GTCGCGGAAGCTGTCGGAAACa < 1:348964/143‑1 (MQ=255)
tttCGCCTGATCTACGGTACGCACGAACGGGTTCATGCTCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGGTTCACTGCCTCACACTCCAGCGCGACACA‑GTCGCGGCAGCTGTCTGAACCATAAAGGACCGAGCCAc > 2:223722/1‑143 (MQ=255)
ccTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACA‑GTCGCGGAAGCTGTCGGAAACATAGCGGCCCGCGCCACGGAAg > 1:276894/1‑143 (MQ=255)
ccTGATCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACA‑GTCGCGGAAGCTGTCGGAAACATAGCGGCCCGCGCCACGGAAg > 1:274847/1‑143 (MQ=255)
tCTACGGTACGCACGAACGGGTTCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACA‑GTCGCGGAAGCTGTCGGAAACATAGCGGCCCGCGCCACGGAAGCCGAg < 1:442019/143‑1 (MQ=255)
aCGGTACGCACGAACGGGATCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGATACCCACTCCAGCGC‑AAACATAATGCTCAAGCTGCAGGTACCCTAGCGGCCCACCCCACGAAAGcagcacaa > 2:101417/1‑136 (MQ=255)
cACGAACGGGAGCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACA‑GTCGCGGAAGCTGTCGGAAACATAGCGGCCCGCGCCACGGAAGCCGAGCATCGGGTtct < 2:353595/143‑1 (MQ=255)
cGGGAGCATGAGCTCAACGGTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACA‑GTCGCGGAAGCTGTCGGAAACATAGCGGCCCGCGCCACGGAAGCCGAGCATCGGGTTCTCTTCAt < 1:344649/143‑1 (MQ=255)
|
GCTCGGCCAGCAAGGCGTTGGACGGGATTTCACACATCATGATGATTTTCAGCCCGTTCTCGCCACGTTTCAGCCCCTGACGCGCCAGTTCTTCAACCACCGCTTTCGCCTGATCTACGGTACGCACGAACGGGATCATGATCTCAACGTTGGTCAGTCCCATGTCGTTGCGCACACGTTTCACTGCTTCACACTCCAGCGCGAAACA‑GTCGCGGAAGCTGTCGGAAACATAGCGGCCCGCGCCACGGAAGCCGAGCATCGGGTTCTCTTCAT > NC_000913/1785045‑1785317
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
